Recent genome wide association studies have led to the reliable identification of multiple genomic loci where the presence of common SNPs is associated with altered risk of a number of common human diseases. These results offer the prospect of new insights into the nature of complex trait disease in general and specific understanding of the mechanisms underlying major common human diseases. Deriving insight into these underlying mechanisms is not trivial, and requires the development and application of a range of computational and experimental techniques. Molecular processes constitute a key part of the multiple level mechanisms by which SNPs influence disease risk, and a full understanding of their contributions is essential to effective investigation of higher level pathwa and subsystems impact, as well as evaluation of potential drug targets. This project focuses on the role of missense SNPs (those that result in an amino acid substitution in a protein) in disease mechanism. It is now clear that this class of SNP plays a substantial role in common disease mechanisms. We focus on loci associated with increased risk of Crohn's disease, where association studies have been particularly successful in identifying disease relevant loci. Previously developed computational methods are used to identify which of these SNPs are expected to have a large impact on the in vivo molecular function of the corresponding protein, and thus are most likely to be involved in disease mechanism. Currently, there are 39 proteins in 25 loci that have candidate high impact missense SNPs. Results of this analysis are combined with other available information to prioritize proteins for experimental study. In order to determine the precise effect on protein function, we will clone, express and purify a number of the high priority proteins and their SNP variants, and investigate in vitro properties, particularl structural stability and interaction with appropriate binding partners. We have demonstrated the power of this strategy for the case of macrophage stimulating factor (MSP), found to carry a candidate mechanism SNP for Crohn's disease, by establishing that binding to a cell surface receptor is impaired, implying down regulation of macrophage activity. Results of the experimental work together with computational modeling and annotation for all the Crohn's disease loci will made available through an online database and annotation facility, so that the results can be maximally exploited.